Population genetic structure and performing assignment test on six Iranian native goats using simple sequence repeat markers

Original scientific paper Journal of Central European Agriculture, 2019, 20(1), p.74-92 DOI: /10.5513/JCEA01/20.1.2011 Population genetic structure and performing assignment test on six Iranian native goats using simple sequence repeat markers Bizhan MAHMOUDI1*, Jamal FAYAZI1, Reza SHOKRI-GHARELO2 and Ghader MANAFIAZAR3,4 Department of Animal science, Agricultural Sciences and Natural Resources University of Khuzestan, Ahvaz, Iran, *correspondence: 1 Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran 2 West Azerbaijan Agriculture and Natural Resource Research Center, Urmia, Iran 3 Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada, T6G 2P5 4 Abstract The native goat breeds could be better managed and their genetic diversity to be conserved through identification of population genetic structure. Total of 299 animals from six goat breeds, which are major native breeds of Iran, were used to study their genetic structure and understand relationship among the breeds using SSR markers on 13 microsatellite loci. The breeds were selected from different geographic regions of Iran. The results indicated that there is high genetic diversity at the population level (HS of 0.78) and at the species level (HT of 0.86). The level of inbreeding was low across the breeds and even genetic diversion was observed among them, indicating a low level of gene flow at the regional scale. Some level of admixtures was observed among breeds, which supported by clustering of the breeds based on their geographic origin. Analysis of the population genetic structure indicated that all breeds are grouped into four clusters. The assignment accuracy per locus ranged from 40.1% (BM4621) to 66.9% (oarJMP23). The assignment power of microsatellites based on the Bayesian method had positive correlation with the number of alleles and gene differentiation coefficient (Gst) per locus. In conclusion, this study provided a genetic profile for the conservation and improvement and origin of the studied breeds. Keywords: conservation, genetic diversity, goat, microsatellite Introduction Goats constitute important source of proteins, having crucial effects on the life of human population especially in less favored regions around the world (Dubeuf et al., 2004). They are one of the well adapted livestock species to various climate regions 74 Original scientific paper DOI: /10.5513/JCEA01/20.1.2011 MAHMOUDI et al.: Population genetic structure and performing assignment test on six Iranian... (Luikart et al., 2001; MacHugh and Bradley, 2001). In addition to the nutrient importance and the high adaptability of goats, they could strongly contribute in controlling weeds, ecosystem preservation, improving wild-life habitants and decreasing the incidences of wildfire (El Aich and Waterhouse, 1999). Developing countries are home to 60% of total of 921 million worldwide. Iran as a country with diverse climates and as a rapidly developing country is home to 22 million goats (Food and Agriculture Organization, 1997). They could be found in various climate regions including cold mountain area (Lorestan province) and very warm prairie (Khozestan province) in Iran (Bizhan, 2011). Goats are considered as multi-purposes animals which are raised for milk, meat, and fiber, and revenue of many nomadic tribes solely depends on this livestock husbandry (Mahmoudi and Babayev, 2009). They are raised nomadically and mainly named by their demographic position. Iranian breeds are identifiable by their physical appearance and production performance (Vahidi et al., 2014). Studying genetic diversity and population structure of goats are very essential from prospective of conversation their invaluable genetic resources (Hedrick, 2011). Native breeds are invaluable resources because of their genetic diversity and adaptation to the environment over the years. In the recent years, however, the diversity of native breeds is concerned since there are non-systematic crossbreeding practices among farmers and there is not any association or organized record track. In the other hand, another factors, such as climate changes, environmental and ecological factors, natural barriers, human activities, migration, gene flow, or combination of these factors, impose these invaluable genetic resources in the risk of elimination (Wright, 1949; Noss, 1990; Frankham et al., 2002). To address the issue of preservation genetic variation of goat breeds, many researches have been conducted in many countries such as Portugal (Bruno-de-Sousa et al., 2011), China (Chen et al., 2005; Di et al., 2011), Europe and the Middle East (Canon et al., 2006), Italia (Sacchi et al., 2005), and Pakistan (Sultana et al., 2003). There is, however, limit reports about the genetic variation and population structure of Iranian native breeds. Vahidi et al. (2014) investigated genetic diversity among seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. They reported that Iranian breeds possess a remarkably genetic diversity within-breed component and also gene flow within and between regions. In previous studies, findings showed that Iranian native breeds, Markhoz (MAR), Najdi (NAJ), Korki Jonub Khorasan (KJK), Taleshi (TAL), Raeini (RAE), and Lori (LOR), are phylogenetically grouped into two cluster. It has also been indicated that there is a signature of bottleneck in Tali and Markhoz populations (Mahmoudi et al., 2012; Mahmoudi et al., 2013; Mahmoudi et al., 2014). The available information about Iranian native goats is not enough to manage and watch genetic resources of goats in Iran. In order to provide knowledge about Iranian native goats, population genetic structure of some dominant breeds of Iran was investigated. This study tests genetic relationships between Iranian native breed populations to discover possible in danger population. 75 Original scientific paper DOI: /10.5513/JCEA01/20.1.2011 MAHMOUDI et al.: Population genetic structure and performing assignment test on six Iranian... Material and methods Breeds and sample collection Six dominant breeds were selected to include in this study. The breeds were Markhoz (MAR), Najdi (NAJ), Korki Jonub Khorasan (KJK), Taleshi (TAL), Raeini (RAE), and Lori (LOR). Markhos breed (MAR) is found in Kurdistan province of Iran and is well known for fine fiber and adaption to the harsh winter of Zagros Mountains. Najdi (NAJ) breed is predominated in Khuzestan province and are reared for milk and fleece. This breed is well adapted to high temperature of over 40 oC for more than 6 months in a year. The Korki Jonub Khorasan (KJK) breed is adapted to southern of Khorasan province, which has cold and hot climate of desert and semi-arid conditions. The Taleshi (TAL) breed is reared in Hormozgan and Kerman provinces and well known for their high milk yield. Whereas in the same region (...truncated)